Biodiversity of marine microbes is safeguarded by phenotypic heterogeneity in ecological traits

Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both phenomena by investigating a non-cooperative game that interpolates between individual-level competitions and species-level outcomes. We identified all equilibrium strategies of the game. These strategies represent the probability distribution of competitive abilities (e.g. traits) and are characterized by maximal phenotypic heterogeneity. They are also neutral towards each other in the sense that an unlimited number of species can co-exist while competing according to the equilibrium strategies. Whereas prior theory predicts that natural selection would minimize trait variation around an optimum value, here we obtained a mathematical proof that species with maximally variable traits are those that endure. This discrepancy may reflect a disparity between predictions from models developed for larger organisms in contrast to our microbe-centric model. Rigorous mathematics proves that phenotypic heterogeneity is itself a mechanistic underpinning of microbial diversity. This discovery has fundamental ramifications for microbial ecology and may represent an adaptive reservoir sheltering biodiversity in changing environmental conditions.

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Emotions and the Micro-Foundations of Commitment Problems

International Organization ◽

10.1017/s0020818316000473 ◽

2017 ◽

Vol 71 (S1) ◽

pp. S189-S218 ◽

Cited By ~ 22

Author(s):

Jonathan Renshon ◽

Julia J. Lee ◽

Dustin Tingley

Keyword(s):

Emotional Arousal ◽

Decision Makers ◽

Behavioral Approach ◽

Large Power ◽

Individual Level ◽

Theoretical Predictions ◽

Affective Influences ◽

The Individual ◽

Commitment Problems

AbstractWhile emotions are widely regarded as integral to the “behavioral approach” to International Relations (IR), a host of fundamental problems have delayed the integration of affective influences into traditional models of IR. We aim to integrate affect by focusing on commitment problems, a body of work that contains strong theoretical predictions about how individual decision makers will and should act. Across two lab experiments, we use a novel experimental protocol that includes a psychophysiological measure of emotional arousal (skin conductance reactivity) to study how individuals react to changes in bargaining power. While we find support for one key pillar of IR theory—individuals do reject offers when they expect the opponent's power to increase—we also find that physiological arousal tampers with individuals’ ability to think strategically in the manner predicted by canonical models. Our follow-up experiment mimics the elements of institutional solutions to commitment problems and finds support for their efficacy on the individual level. Our novel findings suggest that when individuals face large power shifts, emotional arousal short-circuits their ability to “think forward and induct backwards,” suggesting that emotionally aroused individuals are less prone to commitment problems.

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Comment on ''Effects of long-term high CO<sub>2</sub> exposure on two species of coccolithophore'' by Müller et al. (2010)

Biogeosciences ◽

10.5194/bg-7-2199-2010 ◽

2010 ◽

Vol 7 (7) ◽

pp. 2199-2202 ◽

Cited By ~ 2

Author(s):

S. Collins

Keyword(s):

Global Change ◽

Experimental Evolution ◽

Marine Phytoplankton ◽

Model Systems ◽

Price Equation ◽

High Pco2 ◽

Phenotypic Change ◽

Marine Microbes ◽

Marine Microbe

Abstract. Populations can respond to environmental change over tens or hundreds of generations by shifts in phenotype that can be the result of a sustained physiological response, evolutionary (genetic) change, shifts in community composition, or some combination of these factors. Microbes evolve on human timescales, and evolution may contribute to marine phytoplankton responses to global change over the coming decades. However, it is still unknown whether evolutionary responses are likely to contribute significantly to phenotypic change in marine microbial communities under high pCO2 regimes or other aspects of global change. Recent work by Müller et al. (2010) highlights that long-term responses of marine microbes to global change must be empirically measured and the underlying cause of changes in phenotype explained. Here, I briefly discuss how tools from experimental microbial evolution may be used to detect and measure evolutionary responses in marine phytoplankton grown in high CO2 environments and other environments of interest. I outline why the particular biology of marine microbes makes conventional experimental evolution challenging right now and make a case that marine microbes are good candidates for the development of new model systems in experimental evolution. I suggest that "black box" frameworks that focus on partitioning phenotypic change, such as the Price equation, may be useful in cases where direct measurements of evolutionary responses alone are difficult, and that such approaches could be used to test hypotheses about the underlying causes of phenotypic shifts in marine microbe communities responding to global change.

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On the modelling of tropical tree growth: the importance of intra-specific trait variation, non-linear functions and phenotypic integration

Annals of Botany ◽

10.1093/aob/mcaa085 ◽

2020 ◽

Cited By ~ 1

Author(s):

Jie Yang ◽

Xiaoyang Song ◽

Min Cao ◽

Xiaobao Deng ◽

Wenfu Zhang ◽

...

Keyword(s):

Tree Growth ◽

Bayesian Models ◽

Species Level ◽

Linear Functions ◽

Plant Performance ◽

Growth Data ◽

Growth And Survival ◽

Individual Level ◽

The Individual ◽

Individual Trees

Abstract Background and Aims The composition and dynamics of plant communities arise from individual-level demographic outcomes, which are driven by interactions between phenotypes and the environment. Functional traits that can be measured across plants are frequently used to model plant growth and survival. Perhaps surprisingly, species average trait values are often used in these studies and, in some cases, these trait values come from other regions or averages calculated from global databases. This data aggregation potentially results in a large loss of valuable information that probably results in models of plant performance that are weak or even misleading. Methods We present individual-level trait and fine-scale growth data from >500 co-occurring individual trees from 20 species in a Chinese tropical rain forest. We construct Bayesian models of growth informed by theory and construct hierarchical Bayesian models that utilize both individual- and species-level trait data, and compare these models with models only using individual-level data. Key Results We show that trait–growth relationships measured at the individual level vary across species, are often weak using commonly measured traits and do not align with the results of analyses conducted at the species level. However, when we construct individual-level models of growth using leaf area ratio approximations and integrated phenotypes, we generated strong predictive models of tree growth. Conclusions Here, we have shown that individual-level models of tree growth that are built using integrative traits always outperform individual-level models of tree growth that use commonly measured traits. Furthermore, individual-level models, generally, do not support the findings of trait–growth relationships quantified at the species level. This indicates that aggregating trait and growth data to the species level results in poorer and probably misleading models of how traits are related to tree performance.

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Mathematical properties of nested residues and their application to multi-loop scattering amplitudes

Journal of High Energy Physics ◽

10.1007/jhep02(2021)112 ◽

2021 ◽

Vol 2021 (2) ◽

Author(s):

J. Jesús Aguilera-Verdugo ◽

Roger J. Hernández-Pinto ◽

Germán Rodrigo ◽

German F. R. Sborlini ◽

William J. Torres Bobadilla

Keyword(s):

Scattering Amplitudes ◽

Particle Physics ◽

Mathematical Proof ◽

Mathematical Structure ◽

High Energy ◽

The Novel ◽

Feynman Integrals ◽

Mathematical Properties ◽

Theoretical Predictions ◽

Physical Information

Abstract The computation of multi-loop multi-leg scattering amplitudes plays a key role to improve the precision of theoretical predictions for particle physics at high-energy colliders. In this work, we focus on the mathematical properties of the novel integrand-level representation of Feynman integrals, which is based on the Loop-Tree Duality (LTD). We explore the behaviour of the multi-loop iterated residues and explicitly show, by developing a general compact and elegant proof, that contributions associated to displaced poles are cancelled out. The remaining residues, called nested residues as originally introduced in ref. [1], encode the relevant physical information and are naturally mapped onto physical configurations associated to nondisjoint on-shell states. By going further on the mathematical structure of the nested residues, we prove that unphysical singularities vanish, and show how the final expressions can be written by using only causal denominators. In this way, we provide a mathematical proof for the all-loop formulae presented in ref. [2].

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Domino-like propagation of collective U-turns in fish schools

10.1101/138628 ◽

2017 ◽

Cited By ~ 3

Author(s):

Valentin Lecheval ◽

Li Jiang ◽

Pierre Tichit ◽

Clément Sire ◽

Charlotte K. Hemelrijk ◽

...

Keyword(s):

Spin Model ◽

Social Conformity ◽

Fish Schools ◽

Individual Level ◽

Ising Spin ◽

Stochastic Fluctuations ◽

Anticlockwise Direction ◽

Theoretical Predictions ◽

The Individual ◽

Mean Time

AbstractMoving animal groups such as schools of fish or flocks of birds often undergo sudden collective changes of their travelling direction as a consequence of stochastic fluctuations in heading of the individuals. However, the mechanisms by which these behavioural fluctuations arise at the individual level and propagate within a group are still unclear. In the present study, we combine an experimental and theoretical approach to investigate spontaneous collective U-turns in groups of rummy-nose tetra (Hemigrammus rhodostomus) swimming in a ring-shaped tank. U-turns imply that fish switch their heading between the clockwise and anticlockwise direction. We reconstruct trajectories of individuals moving alone and in groups of different sizes. We show that the group decreases its swimming speed before a collective U-turn. This is in agreement with previous theoretical predictions showing that speed decrease facilitates an amplification of fluctuations in heading in the group, which can trigger U-turns. These collective U-turns are mostly initiated by individuals at the front of the group. Once an individual has initiated a U-turn, the new direction propagates through the group from front to back without amplification or dampening, resembling the dynamics of falling dominoes. The mean time between collective U-turns sharply increases as the size of the group increases. We develop an Ising spin model integrating anisotropic and asymmetrical interactions between fish and their tendency to follow the majority of their neighbours nonlinearly (social conformity). The model quantitatively reproduces key features of the dynamics and the frequency of collective U-turns observed in experiments.

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Physiological variation reflects bioclimatic differences in the Drosophila americana species complex

10.1101/453571 ◽

2018 ◽

Author(s):

Jeremy S. Davis ◽

Leonie C. Moyle

Keyword(s):

Natural Selection ◽

Environmental Gradients ◽

Functional Trait ◽

Species Level ◽

Environmental Data ◽

Desiccation Resistance ◽

Uv Resistance ◽

Multiple Traits ◽

Trait Variation ◽

Geographic Space

AbstractBackgroundDisentangling the selective factors shaping adaptive trait variation is an important but challenging task. Many studies—especially in Drosophila—have documented trait variation along latitudinal or altitudinal clines, but frequently lack resolution about specific environmental gradients that could be causal selective agents, and often do not investigate covariation between traits simultaneously. Here we examined variation in multiple macroecological factors across geographic space and their associations with variation in three physiological traits (desiccation resistance, UV resistance, and pigmentation) at both population and species scales, to address the role of abiotic environment in shaping trait variation.ResultsUsing environmental data from collection locations of three North American Drosophila species—D. americana americana, D. americana texana and D. novamexicana—we identified two primary axes of macroecological variation; these differentiated species habitats and were strongly loaded for precipitation and moisture variables. In nine focal populations (three per species) assayed for each trait, we detected significant species-level variation for both desiccation resistance and pigmentation, but not for UV resistance. Species-level trait variation was consistent with differential natural selection imposed by variation in habitat water availability, although patterns of variation differed between desiccation resistance and pigmentation, and we found little evidence for pleiotropy between traits.ConclusionsOur multi-faceted approach enabled us to identify potential agents of natural selection and examine how they might influence the evolution of multiple traits at different evolutionary scales. Our findings highlight that environmental factors influence functional trait variation in ways that can be complex, and point to the importance of studies that examine these relationships at both population- and species-levels.

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Lineage Functional Types (LFTs): Characterizing functional diversity to enhance the representation of ecological behavior in Earth System Models

10.1101/2020.01.01.891705 ◽

2020 ◽

Author(s):

Daniel M. Griffith ◽

Colin Osborne ◽

Erika J. Edwards ◽

Seton Bachle ◽

David J. Beerling ◽

...

Keyword(s):

Functional Diversity ◽

Species Level ◽

Earth System ◽

Trait Variation ◽

System Models ◽

Biogeographic History ◽

Functional Types ◽

Wide Range ◽

Vegetation Models ◽

Earth System Models

SummaryProcess-based vegetation models attempt to represent the wide range of trait variation in biomes by grouping ecologically similar species into plant functional types (PFTs). This approach has been successful in representing many aspects of plant physiology and biophysics, but struggles to capture biogeographic history and ecological dynamics that determine biome boundaries and plant distributions. Grass dominated ecosystems are broadly distributed across all vegetated continents and harbor large functional diversity, yet most Earth System Models (ESMs) summarize grasses into two generic PFTs based primarily on differences between temperate C3 grasses and (sub)tropical C4 grasses. Incorporation of species-level trait variation is an active area of research to enhance the ecological realism of PFTs, which form the basis for vegetation processes and dynamics in ESMs. Using reported measurements, we developed grass functional trait values (physiological, structural, biochemical, anatomical, phenological, and disturbance-related) of dominant lineages to improve ESM representations. Our method is fundamentally different from previous efforts, as it uses phylogenetic relatedness to create lineage-based functional types (LFTs), situated between species-level trait data and PFT-level abstractions, thus providing a realistic representation of functional diversity and opening the door to the development of new vegetation models.

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FuTRES: Functional Trait Resource for Environmental Studies

Biodiversity Information Science and Standards ◽

10.3897/biss.3.37058 ◽

2019 ◽

Vol 3 ◽

Author(s):

Meghan Balk ◽

Ramona Walls ◽

Robert Guralnick ◽

Edward Davis ◽

John Deck ◽

...

Keyword(s):

Entire Range ◽

Environmental Studies ◽

Functional Trait ◽

Species Level ◽

Archaeological Sites ◽

Logical Framework ◽

Semantic Framework ◽

Individual Level ◽

Field Notes ◽

The Individual

Functional traits are the features of organisms that directly interact with the environment. Studying change and variation in these traits across space, time, and taxonomy can inform how species have responded to environmental and climatic change, how communities are assembled, and other eco-evolutionary questions. Trait data are collected at the individual level; however, animal trait databases often report these data at the species level, undermining their value for researchers who want to look at variation within species and rendering trait data ambiguous when taxonomy is updated. Additionally, these data are often recorded in auxiliary fields, such as “field notes” or hidden in supplementary materials or published tables, making them difficult to recover by researchers. Furthermore, animal trait data from paleontological, zooarchaeological (from archaeological sites), and neontological specimens are typically curated in separate forums and formats that are not easily integrated to provide perspective across the entire range of time. We are developing a toolkit to overcome these challenges called FuTRES: Functional Trait Resource for Environmental Studies. We seek to make these data accessible, standardize trait descriptions across Vertebrata, and teach (future) scientists how to create FAIR (findable, accessible, interoperable, and reusable) trait datasets. To make data more FAIR, FuTRES employs ontologies, a logical framework for relating terms to search datasets and standardizing traits across datasets. FuTRES builds off existing ontologies and standards, such as UBERON for anatomical terms and PATO and OBA for trait terms, as well as create new terms that are general enough to be used for all vertebrates and multiple disciplines. This talk will showcase the semantic framework underpinning FuTRES, describe how we are linking diverse trait datasets to ontologies and, therefore, each other, and report the results of a preliminary analysis of integrated datasets.

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Just how big is intraspecific trait variation in basidiomycete wood fungal fruit bodies?

10.1101/593517 ◽

2019 ◽

Author(s):

Samantha K. Dawson ◽

Mari Jönsson

Keyword(s):

Intraspecific Variation ◽

Community Dynamics ◽

Niche Partitioning ◽

Fruit Body ◽

Interspecific Variation ◽

Functional Trait ◽

Species Level ◽

Fungal Ecology ◽

Species Identity ◽

Trait Variation

AbstractAs the use of functional trait approaches is growing in fungal ecology, there is a corresponding need to understand trait variation. Much of trait theory and statistical techniques are built on the assumption that interspecific variation is larger than intraspecific variation. This allows the use of mean trait values for species, which the vast majority of trait studies adopt. We examined the size of intra- vs. inter-specific variation in two wood fungal fruit body traits: size and density. Both coefficients of variation (CV) and Trait Probability Density analyses were used to quantify trait variation. We found that intraspecific variation in fruit body density was more than twice as variable as interspecific variation, and fruit body size was hugely variable (CVs averaged 190%), although interspecific variation was larger. Further, there was a very high degree of overlap in the trait space of species, indicating that there may be little niche partitioning at the species level. These findings show that intraspecific variation is highly important and should be accounted for when using trait approaches to understand fungal ecology. More data on variation of other fungal traits is also desperately needed to ascertain whether the high level of variation found here is typical for fungi. While the need to measure individuals does reduce the ability to generalise at the species level, it does not negate the usefulness of fungal trait measurements. There are two reasons for this: first, the ecology of most fungal species remains poorly known and trait measurements address this gap; and secondly, if trait overlap between species more generally is as much as we found here, then individual measurements may be more helpful than species identity for untangling fungal community dynamics.

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The importance of individual and species-level traits for trophic niches among herbivorous coral reef fishes

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.0307 ◽

2017 ◽

Vol 284 (1856) ◽

pp. 20170307 ◽

Cited By ~ 8

Author(s):

Jacob E. Allgeier ◽

Thomas C. Adam ◽

Deron E. Burkepile

Keyword(s):

Coral Reef ◽

Species Coexistence ◽

Alternative Hypothesis ◽

Reef Fishes ◽

Species Level ◽

Species Variation ◽

Biological Organization ◽

Species Identity ◽

Niche Complementarity ◽

Individual Level

Resolving how species compete and coexist within ecological communities represents a long-standing challenge in ecology. Research efforts have focused on two predominant mechanisms of species coexistence: complementarity and redundancy. But findings also support an alternative hypothesis that within-species variation may be critical for coexistence. Our study focuses on nine closely related and ecologically similar coral reef fish species to test the importance of individual- versus species-level traits in determining the size of dietary, foraging substrate, and behavioural interaction niches. Specifically, we asked: (i) what level of biological organization best describes individual-level niches? and (ii) how are herbivore community niches partitioned among species, and are niche widths driven by species- or individual-level traits? Dietary and foraging substrate niche widths were best described by species identity, but no level of taxonomy explained behavioural interactions. All three niches were dominated by only a few species, contrasting expectations of niche complementarity. Species- and individual-level traits strongly drove foraging substrate and behavioural niches, respectively, whereas the dietary niche was described by both. Our findings underscored the importance of species-level traits for community-level niches, but highlight that individual-level trait variation within a select few species may be a key driver of the overall size of niches.

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